Histolytics

A Python library for scalable panoptic spatial analysis of histological WSIs

Welcome to Histolytics documentation

Introduction

histolytics is a spatial analysis library for histological whole slide images (WSI) library built upon torch, geopandas and libpysal. The library contains multi-task encoder-decoder architectures for panoptic segmentation of WSIs into __geo_interface__-format and a wide array of spatial analysis tools for the resulting segmentation masks.

Features 🌟

• WSI-level panoptic segmentation
• Several panoptic segmentation models for histological WSIs
• Pre-trained models in model-hub. See: histolytics-hub
• Versatile spatial analysis tools for segmented WSIs

Installation 🛠️

pip install histolytics

Getting started with Histolytics

• Segmentation Quick Start
• API Reference

Models 🤖

• Panoptic HoVer-Net
• Panoptic Cellpose
• Panoptic Stardist
• Panoptic CellVit-SAM
• Panoptic CPP-Net

Contributing

We welcome contributions! To get started:

1. Fork the repository and create your branch from main.
2. Make your changes with clear commit messages.
3. Ensure all tests pass and add new tests as needed.
4. Submit a pull request describing your changes.

See the contributing guide for detailed guidelines.

Citation

@article{2025histolytics,
  title={Histolytics: A Panoptic Spatial Analysis Framework for Interpretable Histopathology},
  author={Oskari Lehtonen, Niko Nordlund, Shams Salloum, Ilkka Kalliala, Anni Virtanen, Sampsa Hautaniemi},
  journal={XX},
  volume={XX},
  number={XX},
  pages={XX},
  year={2025},
  publisher={XX}
}